Microbial species in water ecological environment is very large,some of it will be the Potential pathogenic factor for aquiculture.Recent progress in molecular microbial ecology has revealed that traditional culturing methods fail to represent the scope of microbial diversity in nature,it is difficult or time-consuming to search if there some Potential pathogenic microorganism for aquiculture in aquatic water by culturing techniques.To develop methods to rapidly investigate the full extent of microbial diversity and screen Potential pathogenic microorganisms in aquatic water,we get the genome of all microorganism in water samples by high throughput sequencing technology.By using sequence assembly,performed BLAST (blast+) and clustering analysis (Megan) to classify all these genome to species standard.We can find every microorganism that exist in aquatic water on the taxonomy tree,and annotation it.This bioinformatics method that seek out Potential pathogenic microorganism for aquiculture in aquatic water by analyze environment metagenome is rapidly and efficient.